Hi everyone, 

so i have been doing analysis on promoters , SL_promoter_stringset is a list of 1600 promters stringsets, MotifList are a list of pfm for around 100 motifs, namely

'M0006_1.02 ' etc

i am going to see if these motifs are part of the promoters

here is my code

dllm4<-makePriors(SL_promoter_stringset,1) 

dllm5<-toPWM(MotifList,prior = dllm4)

dllm6<-makeBackground(dllm5,bg.seq=SL_promoter_stringset,type = 'logn',bg.len = 100, bg.source = 'all at promoters split into 100bp chunks')

dllm7<-motifEnrichment(sequence = SL_promoter_stringset, pwms = dllm6)

i tried to get the background and did the motifenrichment analysis, so the outcome looks something like this  for 

dllm7$pwms$M0006_1.02

dllm7$pwms$M0006_1.02
An object of class 'PWM'
ID: M0006_1.02
Target name: M0006_1.02
Frequency matrix:
$pfm
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A   25   14   38    0    0   20   16   35   25    18
C   39   72    0   80   96    1   68   35   16    24
G   27   13   61   19    0   71    8   16   43    17
T    9    1    0    2    4    8    8   14   16    41
Position weight matrix (PWM):
$pwm
        [,1]        [,2]        [,3]       [,4]      [,5]       [,6]       [,7]        [,8]       [,9]      [,10]
A -0.5462997 -1.36650370  0.06497302 -6.6724253 -6.658211 -0.8630223 -1.1784698 -0.06684512 -0.5462997 -1.0121416
C  1.5401439  2.42241378 -6.64385619  2.5599365  2.836785 -3.5697404  2.3401083  1.38458592  0.2617849  0.8427707
G  1.0118105 -0.03502867  2.19806183  0.4936162 -6.658211  2.4022734 -0.7263503  0.26178490  1.6805495  0.3485468
T -1.9836158 -4.76039493 -6.64385619 -3.9824608 -3.084600 -2.1464966 -2.1464966 -1.36650370 -1.1784698  0.1592327
With background nucleotide frequencies which also serve as pseudo-count:
$prior.params
        A         C         G         T
0.3667722 0.1332278 0.1332278 0.3667722 

i am wondering if there are any packages or any functions in bioconductor so that i can do further investigation in these motifs and mainly to  visually analyse if these motifs are actually exist in these promoters (i already have a list of promoters as dnastringset) and how they interact with transcription factors. thank you very much

There are functions in PWMEnrich for this, specifically motifScores() and plotMotifScores(). For me see Use case 2 in the PWMEnrich vignette:

http://bioconductor.org/packages/release/bioc/vignettes/PWMEnrich/inst/doc/PWMEnrich.pdf

Cheers, Robert